Package htsjdk.variant.variantcontext.writer

Examples of htsjdk.variant.variantcontext.writer.VariantContextWriter

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    private VariantContextWriter getWriter() {
        SAMSequenceDictionary seqDict = new SAMSequenceDictionary();
        EnumSet<Options> options = VariantContextWriterFactory.DEFAULT_OPTIONS;
        options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
        VariantContextWriter writer = VariantContextWriterFactory.create(outFile, seqDict, options);
        return writer;
    }
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        FeatureCodec codec = CodecFactory.getCodec(inpath, genome);
        AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(inpath, codec, false);
        VCFHeader header0 = (VCFHeader) bfs.getHeader();

        VariantContextWriter writer = getWriter();
        writer.writeHeader(header0);
        writer.close();

        AbstractFeatureReader<Feature, ?> bfs1 = AbstractFeatureReader.getFeatureReader(outFile.getAbsolutePath(), codec, false);
        VCFHeader header1 = (VCFHeader) bfs1.getHeader();

        assertHeadersEquals(header0, header1);
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        AbstractFeatureReader<VCFVariant, ?> bfs = AbstractFeatureReader.getFeatureReader(inpath, codec, false);
        Iterable<VCFVariant> iter0 = bfs.iterator();
        List<VCFVariant> list0 = new ArrayList<VCFVariant>();
        VCFHeader header0 = (VCFHeader) bfs.getHeader();

        VariantContextWriter writer = getWriter();
        writer.writeHeader(header0);
        for (VCFVariant var : iter0) {
            writer.add(var.getVariantContext());
            list0.add(var);
        }
        writer.close();

        AbstractFeatureReader<VCFVariant, ?> bfs1 = AbstractFeatureReader.getFeatureReader(outFile.getAbsolutePath(), codec, false);
        Iterable<VCFVariant> iter1 = bfs1.iterator();
        VCFHeader header1 = (VCFHeader) bfs1.getHeader();
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        SAMSequenceDictionary seqDict = new SAMSequenceDictionary();
        EnumSet<Options> options = VariantContextWriterFactory.DEFAULT_OPTIONS;
        options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
        options.remove(Options.INDEX_ON_THE_FLY);
        VariantContextWriter writer = VariantContextWriterFactory.create(outputStream, seqDict, options);

        writer.writeHeader(this.header);

        while(features.hasNext()){
            writer.add(features.next().getVariantContext());
        }

        return null;
    }
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            outputMultipleBaseCountsWriter = new MultipleBaseCountsWriter(outputMultipleBaseCountsFile);
    }

    private void initializeVcfWriter() {
        // Wrapper VCFWriters will take ownership of inner writers iff: inner writer != origWriter [which wasn't created here]
        VariantContextWriter origWriter = writer;

        if (enableMergePhasedSegregatingPolymorphismsToMNP)
            writer = new MergeSegregatingAlternateAllelesVCFWriter(writer, getToolkit().getGenomeLocParser(), getToolkit().getArguments().referenceFile, maxGenomicDistanceForMNP, logger, writer != origWriter);

        /* Due to discardIrrelevantPhasedSites(), the startDistance spanned by [partiallyPhasedSites.peek(), unphasedSiteQueue.peek()] is <= cacheWindow
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        catch(IOException ex) {
            throw new UserException.CouldNotCreateOutputFile(file, "Unable to open target output stream", ex);
        }

        EnumSet<Options> options = stub.getWriterOptions(indexOnTheFly);
        VariantContextWriter writer = VariantContextWriterFactory.create(file, this.stream, stub.getMasterSequenceDictionary(), stub.getIndexCreator(), options);

        // if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to send to both
        // TODO -- remove me when argument generateShadowBCF is removed
        if ( stub.alsoWriteBCFForTest() && ! VariantContextWriterFactory.isBCFOutput(file, options)) {
            final File bcfFile = BCF2Utils.shadowBCF(file);
            if ( bcfFile != null ) {
                FileOutputStream bcfStream;
                try {
                    bcfStream = new FileOutputStream(bcfFile);
                } catch (FileNotFoundException e) {
                    throw new RuntimeException(bcfFile + ": Unable to create BCF writer", e);
                }

                VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, bcfStream, stub.getMasterSequenceDictionary(), stub.getIndexCreator(), options);
                writer = new TestWriter(writer, bcfWriter);
            }
        }

        return writer;
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        }

        FileOutputStream outputStream = new FileOutputStream(outputFile);
        EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
        final IndexCreator idxCreator = GATKVCFUtils.getIndexCreator(variant_index_type, variant_index_parameter, outputFile, ref.getSequenceDictionary());
        final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options);

        boolean firstFile = true;
        int count = 0;
        while(!priorityQueue.isEmpty() ){
            count++;
            File file = priorityQueue.remove().getSecond();
            if (!file.exists()) {
                throw new UserException(String.format("File %s doesn't exist",file.getAbsolutePath()));
            }
            FeatureReader<VariantContext> reader = getFeatureReader(fileType, file);

            if(count%10 ==0)
                System.out.print(count);
            else
                System.out.print(".");
            if (firstFile){
                VCFHeader header = (VCFHeader)reader.getHeader();
                outputWriter.writeHeader(header);
                firstFile = false;
            }

            Iterator<VariantContext> it = reader.iterator();

            while (it.hasNext()){
                VariantContext vc = it.next();
                outputWriter.add(vc);
            }

            reader.close();

        }
        System.out.println();

        outputWriter.close();

        return 0;
    }
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                                      final boolean createIndex,
                                      final List<File> inputFiles,
                                      final File outputFile) {
        final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterFactory.DEFAULT_OPTIONS);
        if (createIndex) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);
        final VariantContextWriter out = VariantContextWriterFactory.create(outputFile, sequenceDictionary, options);

        final ProgressLogger progress = new ProgressLogger(log, 10000);
        VariantContext lastContext = null;
        File lastFile = null;
        VCFHeader firstHeader = null;
        VariantContextComparator comparator = null;

        for (final File f : inputFiles) {
            log.debug("Gathering from file: ", f.getAbsolutePath());
            final VCFFileReader variantReader = new VCFFileReader(f, false);
            final PeekableIterator<VariantContext> variantIterator = new PeekableIterator<VariantContext>(variantReader.iterator());
            final VCFHeader header = variantReader.getFileHeader();

            if (firstHeader == null) {
                firstHeader = header;
                out.writeHeader(firstHeader);
                comparator = new VariantContextComparator(firstHeader.getContigLines());
            }

            if (lastContext != null && variantIterator.hasNext()) {
                final VariantContext vc = variantIterator.peek();
                if (comparator.compare(vc, lastContext) <= 0) {
                    throw new IllegalStateException("First variant in file " + f.getAbsolutePath() + " is at " + vc.getSource() +
                            " but last variant in earlier file " + lastFile.getAbsolutePath() + " is at " + lastContext.getSource());
                }
            }

            while (variantIterator.hasNext()) {
                lastContext = variantIterator.next();
                out.add(lastContext);
                progress.record(lastContext.getChr(), lastContext.getStart());
            }

            lastFile = f;

            CloserUtil.close(variantIterator);
            CloserUtil.close(variantReader);
        }

        out.close();
    }
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                .setReferenceDictionary(sequenceDictionary);
        if (CREATE_INDEX)
            builder.setOption(Options.INDEX_ON_THE_FLY);
        else
            builder.unsetOption(Options.INDEX_ON_THE_FLY);
        final VariantContextWriter writer = builder.build();

        final VCFHeader header = new VCFHeader(inputVcfHeader.getMetaDataInInputOrder(), SAMPLE);
        writer.writeHeader(header);

        // Go through the input, strip the records and write them to the output
        final CloseableIterator<VariantContext> iterator = reader.iterator();
      while (iterator.hasNext()) {
        final VariantContext full = iterator.next();
            final VariantContext site = subsetToSamplesWithOriginalAnnotations(full, SAMPLE);
            writer.add(site);
            progress.record(site.getChr(), site.getStart());
        }

      CloserUtil.close(iterator);
      CloserUtil.close(reader);
      writer.close();

        return 0;
    }
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        final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterFactory.DEFAULT_OPTIONS);
        if (CREATE_INDEX) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);

        final VCFHeader outHeader = new VCFHeader(header.getMetaDataInInputOrder(), CollectionUtil.makeList(NEW_SAMPLE_NAME));
        final VariantContextWriter out = VariantContextWriterFactory.create(OUTPUT, outHeader.getSequenceDictionary(), options);
        out.writeHeader(outHeader);

        for (final VariantContext ctx : in) {
            out.add(ctx);
        }

        out.close();
        in.close();

        return 0;
    }
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Related Classes of htsjdk.variant.variantcontext.writer.VariantContextWriter

  • org.broad.igv.cli_plugin.VCFEncoder
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage
  • org.broadinstitute.gatk.tools.CatVariants
  • org.broadinstitute.gatk.tools.walkers.phasing.ReadBackedPhasing
  • picard.vcf.filter.FilterVcf
  • picard.vcf.GatherVcfs
  • picard.vcf.MakeSitesOnlyVcf
  • picard.vcf.MergeVcfs
  • picard.vcf.RenameSampleInVcf
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